With the development of molecular biology, it becomes increasingly important to understand the biological complexity systematically and quantitatively. Endogenous molecular-cellular network theory was proposed to depict the core network structure underneath biological system and quantify it by a nonlinear stochastic dynamical system. We review the basic considerations of this theory and several results achieved so far here. Based on this theoretical framework, we may achieve a better understanding of the progression and regression of complex diseases from an adaptive landscape view, make new and practical predictions, and provide some potentialstrategies towards the prevention, diagnosis, and treatment of these diseases.